Accurate Prediction of Docked Protein Structure Similarity

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
Bahar Akbal-DelibasNurit Haspel

Abstract

One of the major challenges for protein-protein docking methods is to accurately discriminate nativelike structures. The protein docking community agrees on the existence of a relationship between various favorable intermolecular interactions (e.g. Van der Waals, electrostatic, desolvation forces, etc.) and the similarity of a conformation to its native structure. Different docking algorithms often formulate this relationship as a weighted sum of selected terms and calibrate their weights against specific training data to evaluate and rank candidate structures. However, the exact form of this relationship is unknown and the accuracy of such methods is impaired by the pervasiveness of false positives. Unlike the conventional scoring functions, we propose a novel machine learning approach that not only ranks the candidate structures relative to each other but also indicates how similar each candidate is to the native conformation. We trained the AccuRMSD neural network with an extensive dataset using the back-propagation learning algorithm. Our method achieved predicting RMSDs of unbound docked complexes with 0.4Å error margin.

References

Aug 15, 2000·Annual Review of Biophysics and Biomolecular Structure·D S Goodsell, A J Olson
Feb 13, 2003·Journal of the American Chemical Society·Cyril DominguezAlexandre M J J Bonvin
Jun 25, 2004·Nucleic Acids Research·Stephen R ComeauCarlos J Camacho
Oct 1, 2004·Journal of Medicinal Chemistry·Anna Maria FerrariBrian K Shoichet
Mar 21, 2006·Current Opinion in Structural Biology·Jeffrey J Gray
Sep 7, 2007·Proteins·Eiji KanamoriKengo Kinoshita
Mar 25, 2008·Computational Biology and Chemistry·Vineet SangarArthur M Lesk
Apr 22, 2008·Nucleic Acids Research·Efrat MashiachHaim J Wolfson
Apr 30, 2008·Nucleic Acids Research·Sergey Lyskov, Jeffrey J Gray
Mar 25, 2010·Journal of Proteome Research·Panagiotis L Kastritis, Alexandre M J J Bonvin
Sep 2, 2010·Proteins·Howook HwangZhiping Weng
Dec 21, 2011·Methods in Molecular Biology·Angela WilkinsOlivier Lichtarge
Jul 20, 2012·Journal of Bioinformatics and Computational Biology·Bahar Akbal-DelibasNurit Haspel
Sep 3, 2013·Proteins·Sjoerd de Vries, Martin Zacharias
Oct 2, 2013·BMC Bioinformatics·Iain H MoalJuan Fernández-Recio
Feb 26, 2014·Proteome Science·Irina Hashmi, Amarda Shehu
Feb 26, 2014·BMC Structural Biology·Bahar Akbal-Delibas, Nurit Haspel
Sep 4, 2015·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Jing HeBrian Chen

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Citations

Feb 6, 2016·Journal of Bioinformatics and Computational Biology·Bahar Akbal-DelibasNurit Haspel
Oct 18, 2016·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Roshanak FarhoodiNurit Haspel

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Software Mentioned

pyDock
ICAR
Attract
AccuRMSD
ClusPro
RosettaDock
SwarmDock
Haddock
ET
ZRank

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